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Method: Genome-wide detection of natural selection in African Americans pre- and post-admixture
- Wenfei Jin,
- Shuhua Xu,
- Haifeng Wang,
- Yongguo Yu,
- Yiping Shen,
- Bailin Wu,
- and Li Jin
Genome Res. March 2012 22: 519-527; Published in Advance November 29, 2011, doi:10.1101/gr.124784.111
...short inversions have been found in one European Figure 1. Genome-wide distribution of European ancestral contributions. Mean European ancestral contribution across 1890 African-American individuals at each SNP. (Green line) Estimated -wide mean European ancestral contribution (21.68%). Blue bands...
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Research: Worldwide patterns of genomic variation and admixture in gray wolves
- Zhenxin Fan,
- Pedro Silva,
- Ilan Gronau,
- Shuoguo Wang,
- Aitor Serres Armero,
- Rena M. Schweizer,
- Oscar Ramirez,
- John Pollinger,
- Marco Galaverni,
- Diego Ortega Del-Vecchyo,
- Lianming Du,
- Wenping Zhang,
- Zhihe Zhang,
- Jinchuan Xing,
- Carles Vilà,
- Tomas Marques-Bonet,
- Raquel Godinho,
- Bisong Yue,
- and Robert K. Wayne
Genome Res. February 2016 26: 163-173; Published in Advance December 17, 2015, doi:10.1101/gr.197517.115
...wolves had nearly fourfold larger Ne (Fig. 6; Supplemental Table S5). The ancestral population of NewWorld wolves had a relatively large effective size of 17,300 individuals, implying a fairly modest bottleneck in the founding of the North American population. However, the two sampled populations have...
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Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
...of high-quality data on variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii. We analyzed whole s of 1142 individual mosquitoes sampled from the wild in 13 African countries, as well as a further 234 individuals comprising parents...
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Research: Rapid coastal spread of First Americans: Novel insights from South America's Southern Cone mitochondrial genomes
- Martin Bodner,
- Ugo A. Perego,
- Gabriela Huber,
- Liane Fendt,
- Alexander W. Röck,
- Bettina Zimmermann,
- Anna Olivieri,
- Alberto Gómez-Carballa,
- Hovirag Lancioni,
- Norman Angerhofer,
- Maria Cecilia Bobillo,
- Daniel Corach,
- Scott R. Woodward,
- Antonio Salas,
- Alessandro Achilli,
- Antonio Torroni,
- Hans-Jürgen Bandelt,
- and Walther Parson
Genome Res. May 2012 22: 811-820; Published in Advance February 14, 2012, doi:10.1101/gr.131722.111
...from Argentinean Mapuche (Ginther et al. 1993), Kolla/Coya (Álvarez-Iglesias et al. 2007), Pilagá and Wichi/Mataco (Cabana et al. 2006), Bolivian Quechua (Gayà-Vidal et al. 2011), and extant Dominican and Dominican Taino (Lalueza-Fox et al. 2001; Tajima et al. 2004), as well as African Brazilian...
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Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
- PingHsun Hsieh,
- August E. Woerner,
- Jeffrey D. Wall,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Ryan N. Gutenkunst,
- and Michael F. Hammer
Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
...@email.arizona.edu Abstract Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings...
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LETTER: A View of Modern Human Origins from Y Chromosome Microsatellite Variation
- Mark Seielstad,
- Endashaw Bekele,
- Muntaser Ibrahim,
- Amadou Touré,
- and Mamadou Traoré
Genome Res. June 1, 1999 9: 558-567; doi:10.1101/gr.9.6.558
...the single loci of mtDNA and the Y chromosome. The earliest studies of nuclear DNA to support a recent African origin were the surveys of RFLPs performed by Luca Cavalli-Sforza and his collaborators ( Mountain et al. 1993 ). Like some studies of classical markers before them, the RFLPs placed the deepest...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...stability.With the ever-growing number of s made available for nonmodel organisms, biologists are now positioned to investigate the interplay between genomic evolution and species diversity. The genomic evolutionary history of some of the most rapidly diversifying lineages on the planet, such as African...
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LETTER: Sequence Variation Within the Fragile X Locus
- Debra J. Mathews,
- Carl Kashuk,
- Gale Brightwell,
- Evan E. Eichler,
- and Aravinda Chakravarti
Genome Res. August 1, 2001 11: 1382-1391; doi:10.1101/gr.172601
...of which are shared with Asians, as noted above. A total of 11 polymorphic sites were found among Europeans, 15 among Africans, 18 among Asians, and 14 among Americans. There are no fixed differences between any of the four geographic groups. The frequency spectrum reveals a relative paucity of singletons...
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LETTER: Detection of Numerous Y Chromosome Biallelic Polymorphisms by Denaturing High-Performance Liquid Chromatography
- Peter A. Underhill,
- Li Jin,
- Alice A. Lin,
- S. Qasim Mehdi,
- Trefor Jenkins,
- Douglas Vollrath,
- Ronald W. Davis,
- L. Luca Cavalli-Sforza,
- and Peter J. Oefner
Genome Res. October 1, 1997 7: 996-1005; doi:10.1101/gr.7.10.996
...insertion ( Hammer and Horai 1995 ), and the third group (C) by M9, an apparently non-African C → G transversion. Although 150 chromosomes within this data set remain indistinguishable from the putative ancestral haplotype A1, the majority ( n = 568) of samples studied are differentiated by one or more...
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Method: Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos
- Daniel Ariad,
- Svetlana Madjunkova,
- Mitko Madjunkov,
- Siwei Chen,
- Rina Abramov,
- Clifford Librach,
- and Rajiv C. McCoy
Genome Res. January 2024 34: 70-84; Published in Advance December 1, 2023, doi:10.1101/gr.278168.123
...this procedure over a range of depths of coverage and across sets of samples from all superpopulations of the 1000 Genomes Project, abbreviated as follows: (AMR) admixed American, (AFR) African, (EAS) East Asian, (EUR) European, (SAS) South Asian.Application to a large PGT-A data setEncouraged by the performance...

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